New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library !
BioRuby project
10 months
303
15
147947
0
0
Parser of scientific names !
Dmitry Mozzherin
23 months
23
3
80913
0
0
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
8 months
26
8
59361
0
0
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
3 years
15
12
54153
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
4 weeks
114
45
49083
0
0
Shintaro Katayama
5 months
1
40208
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
3 years
16
1
36975
0
0
Http requests to entrez e-utilities
Jared Ning
2 years
8
1
34174
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
3 years
14
5
32019
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
6 years
17
5
30425
0
0
Maf parser for BioRuby
Clayton Wheeler
4 years
10
36
27196
0
0
Gff3 parser for big data !
Pjotr Prins
4 years
7
2
25825
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
2 years
13
1
25016
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
4 years
5
...
24073
0
0
Interfaces with biomodel search engine !
Niall Beard
5 years
1
...
23647
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
23 months
1
2
23389
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
5 years
4
2
20905
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
2 years
13
3
20833
0
0
Ruby parsering for obo files !
Matt Yoder
5 years
5
...
20326
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
3 years
10
21
17548
0
0
Data mining algorithms for jRuby
arrigonialberto86
3 years
16
3
17339
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
9 months
11
5
17052
0
0
A fast parser for fastq files
Francesco Strozzi
5 years
10
...
16529
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
4 years
13861
0
0
Low memory sequence emitters
Pjotr Prins
3 years
11
1
13408
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
18 months
42
9
13324
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
5 years
2
1
13060
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
2 years
3
...
12883
0
0
Build genome output files
Michael Barton
3 years
7
...
12448
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
6 years
1
...
12441
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
14 months
12275
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
5 years
29
15
12251
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
4 years
4
...
12072
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
3 months
2
...
12039
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
3 years
11
2
11581
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
6 years
1
...
11357
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
4 years
2
...
11231
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
6 years
4
...
11155
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
4 years
7
1
10899
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
5 years
3
...
10652
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
5 years
8
2
10579
0
0
Parser to work with file formats used in
Ben J Woodcroft
2 years
...
10108
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
2 years
...
10030
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
3 years
...
10021
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
8 months
2
...
9948
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
14 months
1
...
9662
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
4 years
3
...
9385
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
9 years
22
1
9354
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
6 years
4
...
9350
0
0
A general purpose framework for scripted handling of development/stable
mjy
4 years
2
1
8624
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
6 years
1
...
8556
0
0
Read and manipulate cd-hit clusters
George Githinji
4 years
8135
0
0
Ruby binding for samtools tabix
throwern
3 years
5
1
7964
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
6 years
4
...
7903
0
0
A plugin that allows you to parse large
robsyme
6 years
1
...
7643
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
4 years
2
...
7443
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
6 years
10
...
7364
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
23 months
7343
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
15 months
1
...
7123
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
6 years
40
5
6883
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
4 years
13
19
6702
0
0
Next-generation mapping of mutations
Dan MacLean
4 years
2
...
6621
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
3 years
6595
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
5 years
1
1
6591
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
11 months
1
6572
0
0
Ruby binding to the ucsc kent utilities
throwern
4 years
2
...
6514
0
0
Publish scientific results to the semantic web !
Will Strinz
3 years
3
16
6467
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
19 months
1
...
6333
0
0
Bioinformatics triple-store support
Pjotr Prins
5 years
4
1
6080
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
5 years
2
1
6062
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
6 years
1
...
5861
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
4 years
5741
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
4 years
...
5649
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
15 months
...
5506
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
14 months
15
6
5499
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
3 years
1
...
5447
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
5 years
1
...
5265
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
10 months
1
...
5265
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
6 weeks
1
5168
0
12
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
5 years
1
...
5086
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
5 years
2
...
5075
0
0
A protparam compatible utility for BioRuby
hryk
4 years
2
1
5018
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
5 years
1
...
4654
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
4 years
2
...
4498
0
0
Biostars data-mining and statistical analysis
Joachim Baran
3 years
4130
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
22 months
2
1
3910
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
8 years
5
...
3833
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
23 months
2
1
3738
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
19 months
3
...
3625
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
2 months
5
2
3572
0
2
Gggenome Ruby client
Mitsuteru Nakao
3 years
1
...
3564
0
0
Ruby ensembl rest api
Alberto Donizetti
3 years
2
...
3518
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
3 years
6
...
3405
0
0
Generalized linear models for statsample
Ankur Goel
3 years
3381
0
0
Interface for express beta diversity
Ben J. Woodcroft
3 years
...
3188
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
6 years
4
...
3128
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
6 years
3
...
3116
0
0
Bio-repeatmasker
Andrei Rozanski
3 years
...
3110
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
5 years
1
3061
0
0
Helper methods for reading .delta files
robsyme
2 years
...
3015
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
8 years
90
1
3014
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
7 years
1
...
2997
0
0
A parser for cigar format alignments
Ben J Woodcroft
3 years
4
...
2977
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
6 months
3
...
2935
0
0
Web server for bio-samtools
homonecloco
3 years
...
2888
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
6 years
1
...
2886
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
5 years
1
...
2828
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
5 years
2
...
2821
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
5 years
4
...
2797
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
5 years
...
2781
0
0
One-line summary of your gem
Toshiaki Katayama
5 years
1
...
2781
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
5 years
4
...
2743
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
5 years
1
...
2734
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
5 years
1
...
2730
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
5 years
1
...
2721
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
5 years
3
1
2719
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
5 years
1
...
2693
0
0
Build graph with jRuby
Matteo Picciolini
4 years
2518
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
4 years
...
2271
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
13 months
...
2244
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
4 years
2
...
2093
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
2 years
...
2036
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
4 years
...
2007
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
2 years
1970
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
3 years
1
...
1795
0
0
Mine publications for gene names
Pjotr Prins
3 years
1
...
1630
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
2 years
1
...
1533
0
3
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
3 years
1501
0
0
Tools to work with fasta files, indexed with
homonecloco
2 years
...
1461
0
0
Tools to manipulate blat files from the command
homonecloco
2 years
...
1434
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
2 years
...
1399
0
0
Api of picard tool
Natapol Pornputtapong
2 years
1308
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
2 years
1254
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
8 years
1240
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
22 months
1027
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
22 months
...
1022
0
0
Basic wrapper for the kallistio mapper
homonecloco
21 months
1
...
1000
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
18 months
...
840
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
17 months
...
788
0
0
Biosql plugin for BioRuby
BioRuby project
13 months
...
545
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2017-07-24
**) number of commits on GitHub (last 7 days & last 90 days)